Bed file reading error with readTranscriptFeatures()

[gladiagit]

The bed file is downloaded from UCSC. A previous version of the package (1.12) has no issues with reading it but 1.14 fails with the "error in rownames ... invalid rownames length" error . is there a fix for this ?

[al2na]

Can you send a reproducible example ?

On Wed 13. Feb 2019 at 22:08, gladiagit ***@***.***> wrote: The bed file is downloaded from UCSC. A previous version of the package (1.12) has no issues with reading it but 1.14 fails with the "error in rownames ... invalid rownames length" error . is there a fix for this ? [image: image] <https://user-images.githubusercontent.com/18578978/52743935-cf421c80-2fa0-11e9-89b2-7f225b48556b.png> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#181>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAm9EeSS5d4fNtf2QZXMtOStVGwoQaf1ks5vNH7pgaJpZM4a6R3E> .

-- Sent from mobile, excuse the brevity

[gladiagit]

library(genomation)
gene.obj<-readTranscriptFeatures("test.bed")

[katwre]

Hi @gladiagit ,
Are you sure that your input file is in bed format? does it have a header? Could you share it with us or at least few first lines of it?
I checked readTranscriptFeatures function with a bed file (genomation v1.14, R 3.5.1) and it's fine for me.
Kasia

[gladiagit]

The file doesn't have a header and it was downloaded from the genome browser under the BED format output. Github doesn't let me upload that file format so I've changed the extension.
test.bed.txt

[katwre]

I checked your bed file and it's totally fine for me.

> library(genomation)
Loading required package: grid
> readTranscriptFeatures("~/test.bed.txt")
Reading the table...
Calculating intron coordinates...
Calculating exon coordinates...
Calculating TSS coordinates...
Calculating promoter coordinates...
Outputting the final GRangesList...

GRangesList object of length 4:
$exons 
GRanges object with 716 ranges and 2 metadata columns:
        seqnames            ranges strand |     score         name
           <Rle>         <IRanges>  <Rle> | <numeric>  <character>
    [1]        1 88039087-88039214      - |         8 NM_001302773
    [2]        1 88041014-88041072      - |         7 NM_001302773
    [3]        1 88041452-88041552      - |         6 NM_001302773
    [4]        1 88041982-88042048      - |         5 NM_001302773
    [5]        1 88044404-88044751      - |         4 NM_001302773
    ...      ...               ...    ... .       ...          ...
  [712]        2 12324949-12325050      + |         1 NM_001009332
  [713]        2 12398481-12398639      + |         2 NM_001009332
  [714]        2 12425131-12425878      + |         3 NM_001009332
  [715]        2 12487798-12488092      + |         4 NM_001009332
  [716]        2 12488094-12488421      + |         5 NM_001009332

...
<3 more elements>
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths

I guess there is sth wrong with your input file Dependencies/oar3.1_refseq_nochr.bed

Cheers,
Kasia

[methylnick]

I am getting the same error with a refseq file I downloaded from UCSC. looks and checks out to be a bed file.
snippet_hg19.refseq.bed.txt

My Session Info
sessionInfo.txt

[methylnick]

I am getting the same error with a refseq file I downloaded from UCSC. looks and checks out to be a bed file.
snippet_hg19.refseq.bed.txt

My Session Info
sessionInfo.txt

Hmmm, it would appear upgrading R has solved the issue.

R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] grid stats graphics grDevices utils datasets methods base

other attached packages:
[1] genomationData_1.14.0 genomation_1.14.0

loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.12.0 tidyselect_0.2.5 purrr_0.3.2
[4] reshape2_1.4.3 lattice_0.20-38 seqPattern_1.14.0
[7] colorspace_1.4-1 stats4_3.5.3 rtracklayer_1.42.2
[10] yaml_2.2.0 XML_3.98-1.19 rlang_0.3.2
[13] pillar_1.3.1 glue_1.3.1 BiocParallel_1.16.6
[16] BiocGenerics_0.28.0 matrixStats_0.54.0 GenomeInfoDbData_1.2.0
[19] plyr_1.8.4 stringr_1.4.0 zlibbioc_1.28.0
[22] Biostrings_2.50.2 munsell_0.5.0 gtable_0.2.0
[25] Biobase_2.42.0 IRanges_2.16.0 GenomeInfoDb_1.18.2
[28] parallel_3.5.3 Rcpp_1.0.1 KernSmooth_2.23-15
[31] readr_1.3.1 scales_1.0.0 BSgenome_1.50.0
[34] BiocManager_1.30.4 plotrix_3.7-4 DelayedArray_0.8.0
[37] S4Vectors_0.20.1 XVector_0.22.0 Rsamtools_1.34.1
[40] impute_1.56.0 ggplot2_3.1.0 hms_0.4.2
[43] stringi_1.4.3 dplyr_0.8.0.1 GenomicRanges_1.34.0
[46] tools_3.5.3 bitops_1.0-6 magrittr_1.5
[49] lazyeval_0.2.2 RCurl_1.95-4.12 tibble_2.1.1
[52] crayon_1.3.4 pkgconfig_2.0.2 Matrix_1.2-17
[55] gridBase_0.4-7 data.table_1.12.0 assertthat_0.2.1
[58] rstudioapi_0.10 R6_2.4.0 GenomicAlignments_1.18.1
[61] compiler_3.5.3